amongst them, just based on the names, 1000G_indels_for_realignment.hg19.vcf and indels_mills_devine.hg19.sites.vcf look like the files supposed to use for IndelRealigner/RealignerTargetCreator, Could you clarify the exact files for this purpose?

Since for old version, I have used 1000G_phase1.indels.hg19.vcf and Mills_and_1000G_gold_standard.indels.hg19.sites.vcf. and I compared the new and old files, quite different now.

Best Answer

You're correct that we have not yet updated the file names, but they are fairly minor differences. All you need to know really is the difference between the .vcf and the .sites.vcf files: the .vcf files contain the full callset info including genotypes, while the .sites.vcf files don't contain the genotypes, only the variant sites info. The point of having sites-only files is that they're smaller files. For most purposes such as realignment you only need the sites infomation. But you can choose to use either file.

which is exactly what I used for the old version I described in my original comments above. But if we look at the bundle of the new version, those files are gone or at least the names somewhat changed more or less, I copied and pasted again the files in the bundle for the new version as below:

You're correct that we have not yet updated the file names, but they are fairly minor differences. All you need to know really is the difference between the .vcf and the .sites.vcf files: the .vcf files contain the full callset info including genotypes, while the .sites.vcf files don't contain the genotypes, only the variant sites info. The point of having sites-only files is that they're smaller files. For most purposes such as realignment you only need the sites infomation. But you can choose to use either file.

Sorry,. I just realized that your web page is actually the new version. Our own installation has some confusion about the new and old versions, which was caused by our installation staffs. Sorry about confusion. your web page is fine on that.